User: Rory Stark

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Rory Stark2.8k
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CRUK, Cambridge, UK
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2 days, 10 hours ago
Joined:
6 years, 8 months ago
Email:
r*********@cruk.cam.ac.uk

I am Principal Scientist, Computational Biology at the University of Cambridge, leading the Analysis Team in the Bioinformatics Core at Cancer Research UK's Cambridge Institute.

Posts by Rory Stark

<prev • 502 results • page 1 of 51 • next >
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Answer: A: Is it possible to change how DiffBind merge peaks?
... We are looking at exposing this feature in `DiffBind`, but currently there is no way to override the 1bp overlap. If you are able to separately derive a merged consensus set using alternative criteria, not that you can pass it in to `dba.count()` and that set will be used for all the subsequent ste ...
written 6 days ago by Rory Stark2.8k
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Answer: A: diffbind counts as same values
... I suspect this is a normalization issue, where the normalized read values are all the same. You can check this by setting `bNormalized=FALSE` in the call to `dba.report()` to see the "raw" read values. I also see that in the call `dba.count()`, you have set `bScaleControl=FALSE`. As you are subtrac ...
written 6 days ago by Rory Stark2.8k
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Answer: A: Help with DiffBind plotVenn and referencing peak sets in general
... Yes, you can directly specify the peaksets you want to include in the Venn diagram using the `mask` parameter as described in the help page for `dba.plotVenn()`. For example, you can just say: dba.plotVenn(consensus, mask=c(7,26)) ...
written 6 days ago by Rory Stark2.8k
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Answer: A: in diffbind dba.peakset what is the meaning of minOverlap?
... I'm a little unclear of what exactly you are trying to do. Given that you have the same number of peaks for each sample, it looks like you have already counted reads using `dba.count()`, is that correct? In that case you have already formed a consensus set (probably using the default `minOverlap=2` ...
written 6 days ago by Rory Stark2.8k
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Answer: A: diffbind plotVenn by Factor
... In the help page for `dba.plotVenn()`, there is an example of how to do this. In that case, it is based on tissue type (cell line). First the consensus peaks are added of reach tissue type, then the four-way Venn is plotted. This should be done on the peaks themselves, *before* the counting step. H ...
written 6 days ago by Rory Stark2.8k
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Answer: A: diffBind analysis: only one replicate
... Actually, you have no replicates for this TF, only a single sample. Which could be an outlier, you have no way of knowing without replication. Without replicates you can not do any meaningful statistical analysis. You can do things like look at peak overlaps with other factors, or look at relative ...
written 6 weeks ago by Rory Stark2.8k
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Comment: C: diffbind dba.plotvolcano bLabels option use genames instead of numbers
... This is on my list of possible features to add, but there are a number of things ahead of it! The main thing it requires is an interface to add an annotation to the peakset, as most ChIP peak intervals do not correspond directly to annotated genes. ...
written 6 weeks ago by Rory Stark2.8k
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Answer: A: Can we change the name of the ColAttributes in the image generated by dba.plotHe
... Yes you can! You can change the labels used in the plots by setting certain `config` values. For example, see the following code using the sample data supplied with `DiffBind`: data(tamoxifen_analysis) tamoxifen$config$tissue <- "Cell Line" tamoxifen$config$condition <- "Tamoxife ...
written 6 weeks ago by Rory Stark2.8k
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Comment: C: How can I remove the row and column labels/names in the plot() or dba.plotHeatma
... See https://support.bioconductor.org/p/124058/ ...
written 7 weeks ago by Rory Stark2.8k
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Answer: A: Can we control colors for two different colAtributes
... The `colSideCols` parameter can be a list of vectors of colors. Each vector specifies the colors to use for each of the attributes. For example, using the sample data provided with `DiffBind`: data(tamoxifen_counts) plot(tamoxifen, ColAttributes=c(DBA_TISSUE,DBA_CONDITION), colSid ...
written 7 weeks ago by Rory Stark2.8k

Latest awards to Rory Stark

Scholar 10 weeks ago, created an answer that has been accepted. For A: MA plot DiffBind in ggplot2
Scholar 9 months ago, created an answer that has been accepted. For A: MA plot DiffBind in ggplot2
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: diffbind finding not differential site
Popular Question 9 months ago, created a question with more than 1,000 views. For diffbind
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Differential analysis of multiple samples with different time points
Popular Question 9 months ago, created a question with more than 1,000 views. For DiffBind & Chip-exo
Scholar 9 months ago, created an answer that has been accepted. For A: dba.count binding matrix coordinates
Popular Question 9 months ago, created a question with more than 1,000 views. For DiffBind annotation
Popular Question 9 months ago, created a question with more than 1,000 views. For DiffBind Question
Scholar 9 months ago, created an answer that has been accepted. For A: DiffBind differential binding normalization with different levels of binding
Popular Question 9 months ago, created a question with more than 1,000 views. For Diffbind: Binding Affinity Heatmap
Popular Question 11 months ago, created a question with more than 1,000 views. For diffbind
Scholar 11 months ago, created an answer that has been accepted. For A: MA plot DiffBind in ggplot2
Scholar 12 months ago, created an answer that has been accepted. For A: DiffBind differential binding normalization with different levels of binding
Scholar 12 months ago, created an answer that has been accepted. For A: MA plot DiffBind in ggplot2
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Work with GRanges objects in DiffBind
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Differential analysis of multiple samples with different time points
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: diffbind finding not differential site
Scholar 13 months ago, created an answer that has been accepted. For A: MA plot DiffBind in ggplot2
Scholar 16 months ago, created an answer that has been accepted. For A: MA plot DiffBind in ggplot2
Popular Question 2.3 years ago, created a question with more than 1,000 views. For DiffBind Question
Commentator 2.3 years ago, created a comment with at least 3 up-votes. For C: Diffbind - What exactly is a "consensus" peak set?
Scholar 2.3 years ago, created an answer that has been accepted. For A: MA plot DiffBind in ggplot2
Scholar 2.3 years ago, created an answer that has been accepted. For A: DiffBind matrix of values
Popular Question 2.3 years ago, created a question with more than 1,000 views. For diffbind

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